At a currently unknown point in Earth's history, the Super-Ancient Beings discovered the Dark Sun and set about constructing a machine that would repel it before it came too close to the planet. During their endeavors, they constructed tools that would work in unison with the Firestone of the Golden Capstone help to cleansethe Pillars, reveal the locations of each Vertex, the dates each Pillar had to be laid, view the Dark Star and reveal the incantation that would activate the Machine.

Though they were able to prevent the Dark Star from approaching in their time, the Super-Ancient Beings realised that even after they were gone from the Earth, there may yet be intelligent life, and so left the Six Sacred Stones and Pillars so that human kind could use them to aid their attempts to rebuild the Machine.

Eventually, five of the Sacred Stones came to be kept in Egypt under the Pharaoh Khufu's keep (himself apparently being a King of one of the Four Legendary Kingdoms). The remaining Sacred Stone, the Altar Stone, was left to remain at its shrine of Stonehenge. When he rose to power, Rameses II came to refer to the Basin as his own.

Ultimately, however, the priest Thuthmosis stole the Pillars and the Sacred Stones and took them with him as he fled Egypt, unwittingly putting the Earth at greater risk of being destroyed by the Dark Sun.

Because of Thuthmosis's actions, the Sacred Stones were scattered around the known world over the next few thousand years, though the Altar Stone of Stonehenge continued to remain where it had been left for years.

The former priest would claim that a single God had written on the Twin Tablets his Ten Commandments, and they would be held by his descendants until they were stolen and hidden beneath the Churches of Lalibela. The Seeing Stone wound up with the Neetha tribe at the very shrine it was intended to be used at after briefly being stolen away to Delphi. The Philosopher's Stone ended up in the hands of the Chinese Scholar Laozi, who arranged for it to be guarded by a series of traps in a cavern beneath Witch Mountain. The Basin was ultimately obtained by the British, but due to Napoléon Bonaparte's mis-identification of the artefact was left on display at the British Museum under another name. Furthermost away from the other Sacred Stones, the Killing Stone ended up in the hands of the Mayans, who would use the stone in their sacrificial killing rituals until the Americans took possession of it later on.

In the course of their separate research into the Machine, Max Epper and Felix Bonaventura concluded that the Six Sacred Stones were crucial to uncovering the locations of the Vertices and readying the Pillars for laying in the Machine.

The Six Stones are each in some way connected with the Machine, be it the Vertices, the Pillars or providing knowledge relating to the Machine or the Dark Star. For most of the Stones to reveal their true nature, they must be connected with the Firestone (not one of the Sacred Stones), and only one does not require the Firestone to function (the Twin Tablets).

The Philosopher's Stone is intended to cleanse each of the Pillars so that they are ready for placing inside each of the corresponding Vertices. There is a recess inside the Stone, into which the Pillar is placed before being closed by a lid, and the Firestone must then be placed in another, smaller recess in the lid. Following a bright flash of light, the Pillar is changed from a cloudy colour to a shiny translucent glass-like state. How the cleansing process works is unclear, most likely being the result of the Super-Ancient Beings' advanced technology..

The Altar Stone of the Stonehenge temple reveals the location of each of the Vertices. In order for this to work, the Firestone must be placed in a recess in the Altar Stone during a Titanic Rsing, which is when the Dark Star's bent invisible light shines upon Stonehenge. While the Altar Stone itself does not do anything, from its placing upon it, the Firestone shines purple light upon the standing stones, illuminating a strange moss. On each of the ten standing stones, there is the revelation of the seven continents and the three main ocean. The order of the Vertices is shown by a pinpoint of light at its location.

The Killing Stone of the Maya reveals the dates and times that each Pillar must be placed at its corresponding Vertex. The Firestone fits into a recess at the top, and subsequently Mayan symbols start glowing, giving the dates and times. As the Mayan Calendar is similar to the modern calendar, it is easy to calculate the data.

The Delphic Orb is used to see the Dark Star. This is intended to be done at the location which would later become the Neetha Village. Using an inclinometer at the base of the extinct volcano, the Delphic Orb is then placed at the summit with the Firestone placed inside a recess in the bottom of the Orb. When one looks through the inclinometer and the Orb, it acts as a tubeless telescope, and one can see the Dark Star.

The Twin Tablets of Thuthmosis contain an incantation that is to be performed at the last Vertex during the Pillar's placing. Both of the incantations (which is repeated on both Tablets) are written in Thoth, and so while this is the only one of the Sacred Stones that does not require the Firestone to work, only someone who can read the word of Thoth can perform the final ceremony to activate the Machine.

The Basin of Rameses II performs a second cleansing of the latter three Pillars, due to the much harsher light of the Dark Star at the Pillar-placing times. The Basin must be filled with water from the Spring of the Black Poplar, and the Basin has a rectangular recess for the Firestone to fit into. When used with the Firestone, the Pillar (which is to have already been cleansed by the Philosopher's Stone) is to be placed into the Basin so that it is cleansed once again, taking on a slightly more lustrous sheen than the Philosopher's Stone-cleansed Pillar.